title: NHSC_J037_HG_U13Plus_2.CEL

status: Public on Jul 15 2009

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from normal human Schwann cell culture.

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.

scan_protocol: GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)

data_processing: Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used (Brainarray, Hs133P_Hs_REFSEQ_8).

source_name: Culture: normal human Schwann cell

label_protocol: 20ng of total RNA is amplified with Ovation RNA Amplification System V2 (Nugen Technologies, Inc.), and 3.75ug of the resuling amplified cDNA is fragmented and labeled with FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.) and directly used for preparation of hybridization cocktail (please see the Appendix of FL-Ovation cDNA Biotin Module V2 Manual).

extract_protocol: Total RNA was extracted from cells using Qiagen's RNeasy Mini Kit. RNA was isolated from tumors with the RNeasy Micro Kit fibrous tissue protocol as described by the manufacturer.

tag: NHSC


title: WS1 with array type maize from Affymetrix

status: Public on Jul 22 2009

type: RNA

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

molecule: total RNA

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: aerial - Maize plants were grown in culture room conditions with a thermoperiod of 25 celsius day/22 celsius night and a photoperiod of 16h day/8h night. Seeds were sown in pots containing compost (H4-TREF) and fertilized one time a week with Algoflash solution. At 6-7-leaf stage samples (young piled-up internodes) were collected individually and immediatly frozen.

extract_protocol: Pool of extract, 81-L:1ug, 96-L:1ug, 97-L:1ug, WS1:185ug.

treatment_protocol: Name:Early - environmental treatment - hydrometry,drought:time 36hour . short time at REW 20-30 percent

tag: Zea mays, maize, corn  - dev.stage (Boyes et al. Plant Cell 2001):7 or 8 leaves


title: Universal_STD_1

country: USA

description: Gene expression data from whole mouse.

label: biotin

organism: Homo sapiens

source_name: whole mouse reference

tag: reference


title: Uni_STD_2

description: Gene expression data from whole mouse.


title: 90_8

description: Gene expression data from neurofibroma-derived cell culture.

source_name: Culture: MPNST cell line

tag: MPNST cell


title: pNFSC_05.5

source_name: Culture: plexiform neurofibroma-derived Schwann cell

tag: pNFSC


title: pNFSC_97.9_HG_U13Plus_2.CEL


title: Uni_STD_3

description: Gene expression data from whole mouse.


title: NHSC_02.8_HG_U13Plus_2.CEL


title: dNFSC_JLM_HG_U13Plus_2.CEL

source_name: Culture: dermal neurofibroma-derived Schwann cell

tag: dNFSC --


title: 88_3


title: pNFSC_00.13


title: pNF95.3


title: WS2 with array type maize from Affymetrix


title: pNFSC_05.4


title: pNFSC_04.7


title: NHSC_J017


title: Uni_STD_1

description: Gene expression data from whole mouse.


title: dNFSC_ABB


title: NHSC_286


title: N2-3

status: Public on Jul 24 2009

city: Worcester

first: Marian

last: Walhout

state: MA

address: 364 Plantation St - LRB#605

institute: UMASS Medical School

hyb_protocol: Fragmentation, hybridization, and wash were performed as recommended by the Affymetrix GeneChip® Expression Analysis Technical Manual

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: For the normalization and analysis of the microarray data we used R and the affy (Gautier et al., 2004), gcrma (Irizarry et al., 2006) and limma (Smyth, 2004) packages from Bioconductor (www.bioconductor.org). All microarrays for each experiment were normalized using the gcrma package. To avoid artifacts in fold-change due to very low probe intensities in both conditions, we trimmed the data keeping only probe sets that had a mean log2(signal intensity) of the three replicas of 8 or higher, in at least one condition. This threshold was chosen based on the signal intensities of the external polyA RNA and cRNA controls. The trimmed data were analyzed for differential expression using the limma package. We considered as differentially expressed those genes whose probe sets had a P < 0.01 and log2(fold-change) ≥ 0.7. Probe sets were converted to WBGene IDs using the Affymetrix annotation file “Celegans.na26.annot-trimmed.csv” and WormMart. To avoid redundancy we kept only one gene per probe set and one probe set per gene. We also removed genes encoded by the mitochondrial genome. The total number of genes detected was 6,591.

organism: Caenorhabditis elegans

source_name: WT embryos, L1 and L2 larvae, whole animals

label_protocol: For cRNA in vitro transcription/labeling, the Enzo BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo Life Sciences) was used with overnight incubation

growth_protocol: Both wild type and mutant worms were grown on standard worm egg plates; Eggs were harvested by standard bleaching protocol, collected for embryonic RNA isolation, and plated for growing synchronous cultures of worms. L1 and L2 larval worms were collected at the appropriate time points for RNA isolation. Three biological replicates were created for each genotype and life stage and RNA from emrbyos, L1s, and L2s was pooled for each replicate

extract_protocol: RNA isolation was performed as described in Van Gilst, M et al (2005) PLoS Biol

treatment_protocol: Not applicable; grown under standard 20 degree Celsius laboratory conditions

tag: genotype

value: wild type

tag: tissue

value: embryos, L1 and L2 larvae


title: pNF00.6


title: dNFSC_ERS


title: UniversalSTD_3

description: Gene expression data from whole mouse.


title: SCC5N_KO


title: UniversalSTD_2

description: Gene expression data from whole mouse.


title: RMN9N_KO


title: pNF05.3


title: pNF04.4


title: NHSC338


title: MPNST96.2


title: MPNST97.6


title: NHSC323


title: UniversalSTD_1

description: Gene expression data from whole mouse.


title: ADN1N_KO


title: SCC_7N_-l-


title: MGF_33N_+l-

tag: dNFSC +-


title: NHSC_339


title: NHSC216


title: NHSC_771


title: MPNST_94_3


title: NHSC_303


title: pNF03.3


title: Universal_STD_3

description: Gene expression data from whole mouse.


title: CLT_6N_+l-


title: MPNST_02_2


title: MPNST95.3b


title: YST1


title: AIBC_2N_-l-


title: ABC_8N_-l-


title: S520


title: Universal_STD_2

description: Gene expression data from whole mouse.


title: T265


title: ST8814


title: pNF95.6


title: 146-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1

status: Public on Jul 01 2009

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

hyb_protocol: Ten micrograms of the subsequently produced Cy3-aRNA was diluted (1:3) in hybridization buffer (50% formamide, 2.4% SDS, 4X SSPE, 2.5X Denhardt's solution, and 2µl of blocking solution (1µg Cot-1 DNA and 1µg poly (dA)). The probe was then boiled for 1 min and incubated in the dark for 1 h at 50°C prior to hybridization. The slides were prewashed with 0.2% SDS for 2 min, just-boiled Milli-Q water for 2 min, rinsed in 70% ethanol for 2 min, and then dried.  Slides were pre-hybridized in a hybridization oven with a pre-hybridization buffer (33.3% formamide, 1.6% SDS, 2.X SSPE, 1.6X Denhardt’s solution, and 0.1µM salmon sperm DNA) in the dark for 1 h at 50°C.  Slides were then hybridized with Cy-3-aRNA in the dark for 16 h at 50°C.  After the hybridization, slides were rinsed in 2X SSC, 0.1% SDS and soaked in 0.2X SSC, 0.1% SDS for 15 min in the dark at room temperature, followed by a rinse in 0.2X SSC, soaking in 0.2X SSC for 15 min, 0.1X SSC for 15 min and finally Milli-Q water for 5 min in the dark in order to remove carryover SDS.

scan_protocol: The micorarray were scanned using ScanArray Express and SpotArray software at 70 V photomultiplier tube (PMT) gain and the raw data was quantified with QuantArray software (Perkin Elmer).

data_processing: The data were background corrected using the normexp method and a print-order loess normalization was carried out.  Next, genes which the 4 replicates did not show intensity higher than three times the average intensity of the non-oyster genes present in the slides  in at least 10% of the slides in the experiment were disregarded.  Last, the remaining data were variance stabilization normalized (vsn).

organism: Crassostrea virginica

label_protocol: One microgram of total RNA was used to produce Cy3-labeled aminoallyl RNA (Cy3-aRNA) probe using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion), according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from RNAlater (Ambion), stabilized oyster tissues using Qiagen's RNeasy Mini kits with an on- column DNase (Qiagen) treatment.  Extracted RNA was quantified by absorbance at 260nm using a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies).

value: Hepatopancreas

tag: location

value: Burnett

tag: creek order


title: 152-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1

value: New Market


title: 151-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 144-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 148-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: STS26T


title: S462


title: 149-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 150-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 143-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 142-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 147-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 145-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 140-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 139-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 141-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 138-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 137-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 135-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 136-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 134-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 132-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 126-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 118-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1

value: Postell


title: 133-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 120-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 130-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 119-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 117-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 129-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 1


title: 122-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 125-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 116-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 131-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 121-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 128-H: tissue: Hepatopancreas; Location: Burnett; Creek Order: 2


title: 114-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 115-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 123-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 112-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 124-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 111-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 110-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 109-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 108-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 104-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 103-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 094-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1

value: Oakdale


title: 098-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 089-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 106-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 100-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 101-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 102-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 091-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 095-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 099-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 097-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 092-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 096-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 090-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 093-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 083-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 085-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 084-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 086-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 113-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 088-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 105-H: tissue: Hepatopancreas; Location: Postell; Creek Order: 1


title: 077-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 075-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3

value: Duplin


title: 079-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 081-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 080-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 076-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 072-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 067-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 068-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 070-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 069-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 078-H: tissue: Hepatopancreas; Location: Oakdale; Creek Order: 1


title: 065-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 063-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 066-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 071-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 060-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 074-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 058-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 061-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 059-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 064-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 073-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 057-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 054-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 050-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1

value: Village


title: 055-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 047-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 045-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 053-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 049-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 051-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 1


title: 044-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 052-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 048-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 046-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 040-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 039-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 037-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 043-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 056-H: tissue: Hepatopancreas; Location: Duplin; Creek Order: 3


title: 041-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 034-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 038-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 036-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 035-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 033-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 042-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 029-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 027-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 031-H: tissue: Hepatopancreas; Location: Village; Creek Order: 2


title: 032-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 025-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3

value: Guerin


title: 028-H: tissue: Hepatopancreas; Location: Village; Creek Order: 3


title: 026-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 022-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 021-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 030-H: tissue: Hepatopancreas; Location: Village; Creek Order: 1


title: 024-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 014-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 015-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 017-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 012-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 010-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 013-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 020-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 009-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 008-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 018-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 005-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 019-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 016-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 003-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 1


title: 274-G: tissue: Gill; Location: James Island; Creek Order: 3

value: Gill

value: James Island


title: 001-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 273-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 271-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 270-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 275-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 004-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 2


title: 268-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 269-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 261-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 272-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 262-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 265-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 259-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 257-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 255-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 267-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 002-H: tissue: Hepatopancreas; Location: Guerin; Creek Order: 3


title: 258-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 260-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 254-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 266-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 264-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 252-G: tissue: Gill; Location: James Island; Creek Order: 2


title: 253-G: tissue: Gill; Location: James Island; Creek Order: 3


title: 249-G: tissue: Gill; Location: Whiskey; Creek Order: 2

value: Whiskey


title: 247-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 246-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 245-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 248-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 232-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 241-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 234-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 244-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 237-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 229-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 251-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 227-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 228-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 231-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 236-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 240-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 242-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 238-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 250-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 225-G: tissue: Gill; Location: Masonboro; Creek Order: 1

value: Masonboro


title: 233-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 230-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 243-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 239-G: tissue: Gill; Location: Whiskey; Creek Order: 2


title: 226-G: tissue: Gill; Location: Whiskey; Creek Order: 1


title: 224-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 216-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 213-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 217-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 219-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 212-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 223-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 215-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 222-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 209-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 221-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 207-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 214-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 210-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 208-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 203-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 220-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 211-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 202-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 218-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 206-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 204-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 205-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 201-G: tissue: Gill; Location: Masonboro; Creek Order: 1


title: 197-G: tissue: Gill; Location: Hewletts; Creek Order: 1

value: Hewletts


title: 193-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 200-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 195-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 196-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 188-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 187-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 186-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 263-G: tissue: Gill; Location: James Island; Creek Order: 1


title: 181-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 192-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 189-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 180-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 194-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 182-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 185-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 198-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 190-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 179-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 178-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 191-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 177-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 183-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 184-G: tissue: Gill; Location: Hewletts; Creek Order: 2


title: 169-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 176-G: tissue: Gill; Location: Hewletts; Creek Order: 1


title: 172-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 175-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 174-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 166-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 170-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 173-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 171-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 161-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 165-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 168-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 167-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 163-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 162-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 153-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 158-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 160-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 156-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 154-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 159-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 157-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 155-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 164-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 150-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 152-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 149-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 148-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 141-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 143-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 144-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 147-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 145-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 142-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 146-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 139-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 130-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 137-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 135-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 140-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 138-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 136-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 134-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 131-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 127-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 129-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 128-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 125-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 132-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 126-G: tissue: Gill; Location: Burnett; Creek Order: 1


title: 151-G: tissue: Gill; Location: New Market; Creek Order: 1


title: 124-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 121-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 120-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 123-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 122-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 119-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 118-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 116-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 117-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 112-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 110-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 115-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 113-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 111-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 109-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 104-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 107-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 114-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 106-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 105-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 101-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 099-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 102-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 100-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 098-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 097-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 095-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 093-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 090-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 103-G: tissue: Gill; Location: Postell; Creek Order: 1


title: 092-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 091-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 089-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 087-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 085-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 088-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 086-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 079-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 084-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 080-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 078-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 083-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 082-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 077-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 075-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 076-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 073-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 074-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 071-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 072-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 068-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 069-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 070-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 066-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 064-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 057-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 067-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 061-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 060-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 065-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 062-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 063-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 059-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 058-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 055-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 054-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 056-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 053-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 052-G: tissue: Gill; Location: Duplin; Creek Order: 3


title: 049-G: tissue: Gill; Location: Village; Creek Order: 3


title: 050-G: tissue: Gill; Location: Village; Creek Order: 1


title: 051-G: tissue: Gill; Location: Duplin; Creek Order: 1


title: 047-G: tissue: Gill; Location: Village; Creek Order: 2


title: 039-G: tissue: Gill; Location: Village; Creek Order: 1


title: 036-G: tissue: Gill; Location: Village; Creek Order: 2


title: 038-G: tissue: Gill; Location: Village; Creek Order: 3


title: 133-G: tissue: Gill; Location: Burnett; Creek Order: 2


title: 043-G: tissue: Gill; Location: Village; Creek Order: 3


title: 040-G: tissue: Gill; Location: Village; Creek Order: 2


title: 048-G: tissue: Gill; Location: Village; Creek Order: 2


title: 044-G: tissue: Gill; Location: Village; Creek Order: 1


title: 042-G: tissue: Gill; Location: Village; Creek Order: 2


title: 037-G: tissue: Gill; Location: Village; Creek Order: 2


title: 041-G: tissue: Gill; Location: Village; Creek Order: 3


title: 034-G: tissue: Gill; Location: Village; Creek Order: 3


title: 045-G: tissue: Gill; Location: Village; Creek Order: 3


title: 046-G: tissue: Gill; Location: Village; Creek Order: 1


title: 032-G: tissue: Gill; Location: Village; Creek Order: 1


title: 081-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 030-G: tissue: Gill; Location: Village; Creek Order: 1


title: 094-G: tissue: Gill; Location: Oakdale; Creek Order: 1


title: 033-G: tissue: Gill; Location: Village; Creek Order: 1


title: 031-G: tissue: Gill; Location: Village; Creek Order: 2


title: 029-G: tissue: Gill; Location: Village; Creek Order: 2


title: 027-G: tissue: Gill; Location: Village; Creek Order: 3


title: 026-G: tissue: Gill; Location: Village; Creek Order: 1


title: 023-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 025-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 017-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 024-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 020-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 016-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 019-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 021-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 018-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 022-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 007-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 008-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 014-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 012-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 010-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 015-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 013-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 005-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 004-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 028-G: tissue: Gill; Location: Village; Creek Order: 3


title: 002-G: tissue: Gill; Location: Guerin; Creek Order: 3


title: 001-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 035-G: tissue: Gill; Location: Village; Creek Order: 1


title: 272-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 003-G: tissue: Gill; Location: Guerin; Creek Order: 1


title: 274-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 263-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 265-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 262-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 267-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 266-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 264-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 258-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 275-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 260-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 269-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 271-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 273-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 259-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 268-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 270-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 261-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 257-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 256-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 251-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 252-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 255-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 2


title: 253-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 3


title: 009-G: tissue: Gill; Location: Guerin; Creek Order: 2


title: 246-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 249-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 244-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 245-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 248-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 243-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 247-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 242-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 250-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 241-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 254-H: tissue: Hepatopancreas; Location: James Island; Creek Order: 1


title: 240-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 235-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 236-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 239-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 237-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 234-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 238-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 232-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 233-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 230-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 231-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 229-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 227-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 2


title: 226-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 225-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 228-H: tissue: Hepatopancreas; Location: Whiskey; Creek Order: 1


title: 222-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 220-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 218-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 224-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 221-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 217-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 223-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 219-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 216-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 214-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 212-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 205-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 215-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 209-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 213-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 208-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 211-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 210-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 206-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 204-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 207-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 203-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 201-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 197-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 200-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 202-H: tissue: Hepatopancreas; Location: Masonboro; Creek Order: 1


title: 199-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 193-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 196-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 195-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 192-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 190-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 188-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 189-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 185-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 194-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 184-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 182-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 181-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 191-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 187-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 186-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 183-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 198-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 180-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 179-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 175-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 176-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 178-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 2


title: 177-H: tissue: Hepatopancreas; Location: Hewletts; Creek Order: 1


title: 174-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 173-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 165-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 172-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 158-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 161-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 162-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 164-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 171-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 159-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 167-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 160-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 169-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 163-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 156-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 157-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 170-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 154-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 155-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 153-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 168-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: 166-H: tissue: Hepatopancreas; Location: New Market; Creek Order: 1


title: Meiosis 1.5 hours Replicate 3

type: genomic

city: Chicago

first: Sean

middle: Erik

last: Hanlon

state: IL

address: 920 E. 58th Street – CLSC 515E

department: Department of Human Genetics

institute: University of Chicago

description: FAIRE Meiosis Time Course - Meiosis 1.5 hours Replicate 3

hyb_protocol: Four micrograms of fluorescently labeled reference DNA and four micrograms of fluorescently labeled FAIRE DNA were used in the hybridization. Samples were competitively hybridized with the reference at 52C for 16 hours in a Maui hybridization chamber to yeast whole genome 4 x 44k tiling microarrays (Agilent; ~270 bp resolution).

scan_protocol: The arrays were scanned with an Axon 4000B scanner, and data was extracted using GenePix 6.0 software.

data_processing: Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, or with a background corrected sum of medians for both channels less than 500, were excluded from analysis (flagged as bad in GenePix). Additionally, those probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (Cy5/Cy3) for each probe was converted to a log2 ratio. These log2 ratios (Cy5/Cy3) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.

molecule: genomic DNA

organism: Saccharomyces cerevisiae SK1

source_name: Genomic DNA prepped from unfixed (no Formaldehyde) sample

label_protocol: ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy3 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.

growth_protocol: Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8.

extract_protocol: 100 ml of UNFIXED cells were washed twice with 1X cold PBS. The cells were lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. We conducted a phenol-chloroform extraction on the UNFIXED samples to remove proteins. The resulting sonicated genomic DNA was precipitated with isopropanol and resuspended in 10 mM Tris-Cl pH 7.4.

tag: strain

source_name: FAIRE Enriched DNA from cells 15hr after transfer to sporulation media (SM)

label_protocol: ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy5 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.

growth_protocol: Synchronous sporulation was carried out by using YPD overnight cultures of wild-type cells to inoculate YPA (1% yeast extract, 2% peptone, 2% potassium acetate) cultures at an OD600 of 0.1. YPA cultures were grown at 30C to an OD600 of 0.8-1.2 (about 16 hours). Cells were collected by centrifugation and washed with SM (2% potassium acetate). The cells were resuspended at an OD600 of 2.0 in SM (~600ml) and incubated in 2L flasks at 30C with shaking at 265 rpm.

extract_protocol: 50 ml of cells were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. The samples were then snap frozen in a dry ice/ethanol bath and stored at -80C. FAIRE was carried out as described (Hogan, Lee and Lieb 2006). Briefly, cells were thawed and lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. We conducted a phenol-chloroform extraction on the crosslinked samples (1 mg of extract) to remove proteins and protein-associated DNA. The resulting DNA samples were further purified using Zymo Clean and Concentrator kit.


title: Meiosis 3 hours Replicate 2

description: FAIRE Meiosis Time Course - Meiosis 3 hours Replicate 2

source_name: FAIRE Enriched DNA from cells 3hr after transfer to sporulation media (SM)


title: Meiosis 0 hours Replicate 1

description: FAIRE Meiosis Time Course - Meiosis 0 hours Replicate 1

source_name: FAIRE Enriched DNA from cells 0hr after transfer to sporulation media (SM)


title: Meiosis 0 hours Replicate 3

description: FAIRE Meiosis Time Course - Meiosis 0 hours Replicate 3


title: Meiosis 1.5 hours Replicate 1

description: FAIRE Meiosis Time Course - Meiosis 1.5 hours Replicate 1


title: Meiosis 3 hours Replicate 3

description: FAIRE Meiosis Time Course - Meiosis 3 hours Replicate 3


title: Meiosis 3 hours Replicate 1

description: FAIRE Meiosis Time Course - Meiosis 3 hours Replicate 1


title: M015

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: The subject was infected with B.pseudomallei

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

source_name: Whole blood from patient with septicemic melioidosis

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: Tempus Spin Isolation Kit

tag: Age

tag: Gender

value: M

tag: Ethnicity

value: Not Hispanic or Latino

tag: Race

value: Asian

tag: Illness

value: Sepsis/Melioidosis

tag: Treatment

value: Bactrim, Ceftazidime

tag: Pathogen


title: YPD Replicate 2

description: FAIRE Meiosis Time Course - YPD Replicate 2

source_name: FAIRE Enriched DNA from cells growing logarithmically (vegetative) in YPD

extract_protocol: 100 ml of cells were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. The samples were then snap frozen in a dry ice/ethanol bath and stored at -80C. FAIRE was carried out as described (Hogan, Lee and Lieb 2006). Briefly, cells were thawed and lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. We conducted a phenol-chloroform extraction on the crosslinked samples (1 mg of extract) to remove proteins and protein-associated DNA. The resulting DNA samples were further purified using Zymo Clean and Concentrator kit.


title: DM005

description: The subject diagnosted type 2 diabetes

source_name: Whole blood from non-infected patient with type 2 diabetes

value: F

value: Control/type 2 diabetes


title: R006

description: The subject had recovered from melioidosis

source_name: Whole blood from patient who had recovered from melioidosis

value: Control/Recovery


title: Meiosis 0 hours Replicate 2

description: FAIRE Meiosis Time Course - Meiosis 0 hours Replicate 2


title: I015

description: The subject was infected with C.albicans

source_name: Whole blood from septic patient with other infections

value: Sepsis/Other infections

value: Ceftazidime


title: I012


title: I014

description: The subject was infected with Salmonella spp.

value: Ceftriaxone, Ceftazidime, Levofloxacin

value: Salmonella spp.


title: M014

value: Cloxacilin,Ceftazidime


title: YPD Replicate 3

description: FAIRE Meiosis Time Course - YPD Replicate 3


title: R005


title: YPD Replicate 1

description: FAIRE Meiosis Time Course - YPD Replicate 1


title: pcDNA3(CT2)

city: Houston

first: Marco

last: Sardiello

address: One Baylor Plaza

department: MHG

institute: Baylor College of Medicine

description: in situ oligonucleotide

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Analysis by RMA.

source_name: Human cell line

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was obtained using the RNeasy kit (Quiagen) according to the manufacturer’s instructions.

tag: cell line

value: HeLa


title: pcDNA3(CT3)

description: in situ oligonucleotide


title: DM006

description: The subject diagnosted type 2 diabetes


title: I013

description: The subject was infected with Corynebacterium spp.

value: Ceftazidime, Clarithromycin

value: Corynebacterium spp.


title: Meiosis 1.5 hours Replicate 2

description: FAIRE Meiosis Time Course - Meiosis 1.5 hours Replicate 2


title: M012

value: Sulperazone, Bactrim,Cetazidime


title: pcDNA3(CT1)

description: in situ oligonucleotide


title: TFEB_Overexpression(S3)

description: in situ oligonucleotide


title: R004

value: M


title: I011

description: The subject was infected with E.coli

value: Not Hispanic or Latino


title: TFEB_Overexpression(S1)

description: in situ oligonucleotide


title: I010

description: The subject was infected with E.coli

value: Asian

value: Ceftriaxone


title: TFEB_Overexpression(S2)

description: in situ oligonucleotide


title: M010

value: Sepsis/Melioidosis

value: Ceftriaxone, Ceftazidime, Doxycycline


title: M009

value: F

value: Sulperazone


title: R003

value: Control/Recovery


title: I009

description: The subject was infected with Staphylococcus aureus

value: Sepsis/Other infections

value: Ceftazidime, Cloxacillin

value: Staphylococcus aureus


title: I007


title: DM003

description: The subject diagnosted type 2 diabetes

value: Control/type 2 diabetes


title: M008

value: Ceftazidime, Bactrim


title: DM002

description: The subject diagnosted type 2 diabetes


title: M006


title: I006

value: Ceftriaxone, Sulperazone, Bactrim


title: M007

value: Ceftazidime, Tazocin


title: M003

value: Ceftazidime


title: DM004

description: The subject diagnosted type 2 diabetes

value: M


title: M002

value: Not Hispanic or Latino

value: Ceftriaxone, Ceftazidime


title: I004

description: The subject was infected with Salmonella serotype B

value: Asian

value: Cloxacillin, Ceftriaxone

value: Salmonella serotype B


title: M001

value: Sepsis/Melioidosis


title: M030

value: Ceftazidime, Ceftriazone


title: I001

description: The subject was infected with Streptococcus non gr.A or gr.B

value: Ceftriaxone

value: Streptococcus non A,B


title: M029


title: I026

description: The subject was infected with K.pneumoniae

value: Sepsis/Other infections

value: Ceftriaxone, Ceftazidime, Bactrim


title: I008

description: The subject was infected with E.coli

value: F

value: Bactrim, Ceftazidime


title: M028

value: Ceftazidime, levofloxacin, Bactrim


title: M027

value: Ceftriaxone, Ceftazidime, Meropenem


title: I002

description: The subject was infected with A.baumannii

value: Ceftriaxone,Bactrim

value: Acinetobactor baumannii


title: I024

description: The subject was infected with Staphylococcus coagulase negative

value: M

value: Not Hispanic or Latino

value: Meropenem,Ceftazidime

value: Staphylococcus coagulase negative


title: DM008

description: The subject diagnosted type 2 diabetes

value: Asian

value: Control/type 2 diabetes


title: M026

value: Sepsis/Melioidosis

value: Ceftazidime, Doxycycline, Bactrim


title: H004

description: Healthy donor

source_name: Whole blood from healthy donor

value: Control/healthy


title: H002

description: Healthy donor


title: I018

value: Sepsis/Other infections

value: Vancomycin


title: M021

value: F

value: Ceftriaxone, Ceftazidime


title: I025

description: The subject was infected with S.pneumoniae

value: Ceftriaxone, Meropenem


title: M025

description: The subject was infected with B.pseudomallei

value: Ceftazidime


title: I022


title: R010

description: Control/Recovery

value: Control/Recovery


title: I023

description: The subject was infected with E.coli

value: Doxycycline,Ceftazidime


title: M024

value: M

value: Meropenem


title: I021

description: The subject was infected with Enterococcus spp.

value: Not Hispanic or Latino

value: Ceftazidime,Cloxacilin

value: Enterococcus spp.


title: I020

value: Asian

value: Ceftazidime,Ceftriaxone

value: Staphylococcus coagulase negative


title: M023

value: Sepsis/Melioidosis

value: Bactrim, Ceftazidime


title: R009

description: The subject had recovered from melioidosis


title: R008

description: Control/Recovery


title: R007


title: H001

description: Healthy donor

value: Control/healthy


title: DM007

description: The subject diagnosted type 2 diabetes

value: F

value: Control/type 2 diabetes


title: I019

value: Sepsis/Other infections

value: Cloxacillin, Ceftazidime

value: Staphylococcus aureus


title: Rerun_M006

hyb_protocol: HumanHT-12 Expression BeadChip

scan_protocol: Illumina BeadScan Version 3.5.49.29917  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 3.1.3.0 using the average chip normalization method.

value: Ceftriaxone


title: Rerun_I001

value: M

value: Streptococcus non A,B


title: I017

value: Not Hispanic or Latino


title: M017

value: Norfloxacin, Ceftazolin


title: Rerun_I010

description: The subject was infected with E.coli


title: Rerun_M001

value: Ceftazidime, Bactrim


title: M022

value: Asian

value: Ceftazidime, Cactrim


title: M020

value: Ceftriaxone,Doxycycline, Ceftazidime


title: Rerun_M014

value: Sepsis/Melioidosis

value: Cloxacilin,Ceftazidime


title: I016

value: Ceftazidime,Bactrim,Sulperazole

value: Staphylococcus coagulase negative


title: M016

value: Ceftazidime, Bactrim, Doxycycline


title: Rerun_I008

description: The subject was infected with E.coli

value: F

value: Sepsis/Other infections

value: Bactrim, Ceftazidime


title: Rerun_I012

value: Ceftazidime


title: Rerun_M002

value: Ceftriaxone, Ceftazidime


title: Rerun_M009

value: Sulperazone


title: Rerun_M012

value: M

value: Not Hispanic or Latino

value: Sulperazone, Bactrim,Cetazidime


title: Rerun_I009

value: Asian

value: Ceftazidime, Cloxacillin

value: Staphylococcus aureus


title: Rerun_I014

value: Ceftriaxone, Ceftazidime, Levofloxacin

value: Salmonella spp.


title: DM013

description: The subject diagnosted type 2 diabetes

value: Control/type 2 diabetes

tag: Treatment:

tag: Pathogen:


title: DM009

description: The subject diagnosted type 2 diabetes


title: Rerun_M007

value: Sepsis/Melioidosis

value: Ceftazidime, Tazocin


title: DM010

description: The subject diagnosted type 2 diabetes

value: F


title: Rerun_M008

value: Ceftazidime, Bactrim


title: DM012

description: The subject diagnosted type 2 diabetes


title: DM011

description: The subject diagnosted type 2 diabetes


title: H006

description: Healthy donor

value: Control/healthy


title: H008

description: Healthy donor


title: H009

description: Healthy donor


title: M038


title: M035

value: Ceftriaxone, Ceftazidime, Fortum


title: M033

value: Fortum ,  Sulperazone, Bactrim, Ciprofloxacin


title: M031

value: Fortum, Bactrim, Trazocin


title: M036

value: Ceftriaxone, Ceftazidime


title: I034

description: The subject was infected with Aeromonas hydrophila

value: M

value: Not Hispanic or Latino

value: Sepsis/Other infections

value: Tazocin

value: Aeromonas hydrophila


title: M032

value: Asian

value: Fortum , Doxycycline, Sulperazone


title: I031

description: The subject was infected with Enterococcus spp

value: Fortum

value: Enterococcus spp


title: H007

description: Healthy donor


title: M034

value: Sepsis/Melioidosis

value: Fortum, Bactrim, Ceftazidime, Ceftriaxone


title: H005

description: Healthy donor


title: I032

description: The subject was infected with Enterococcus faecium

value: F

value: Fortum, Tazocin

value: Enterococcus faecium


title: M037

value: Bactrim, Fortum, Cloxacillin


title: I033

description: The subject was infected with E. coli

value: Tazocin, Ceftriaxone,  Fortum

value: E. coli


title: I029

description: The subject was infected with taphylococcus aureus

value: Fortum,Ceftriaxone,Tazocin

value: Staphylococcus aureus


title: I027

description: The subject was infected with E.coli

value: Not Hispanic or Latino

value: Sepsis/Other infections

value: Fortum, Ceftriaxone


title: Si+ B+ rep2

status: Public on Jun 30 2009

city: Jouy en Josas

first: Florian

last: Chain

address: Domaine de Vilvert

department: Institut Micalis

hyb_protocol: The labelled samples were added to an Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Santa Clara, CA, USA), according to the manufacturer’s instructions. The chips were hybridized for 16 h at 45 °C in a rotisserie oven at 60 rpm

scan_protocol: Following hybridization, the arrays were washed and stained in an Affymetrix Fluidics Station 450, according to the standard protocol from Affymetrix, and scanned using an Affymetrix Scanner 3000.

data_processing: The R 2.6 software and Bioconductor were used to perform data analysis using dedicated packages Limma , Affy , and AffyPLM available on the Bioconductor website (http://www.bioconductor.org/). Data quality assessment was performed as described. These packages were also used to correct for background (RMA method), normalize the microarray data (quantile method) and generate lists of differentially expressed genes according to the fold change and t-test p-values.

organism: Triticum aestivum

source_name: silicon, disease inoculation

label_protocol: Biotin-labeled cRNAs were synthesized using MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, Tx, USA) following the manufacturer’s instructions using 1 µg total RNA. Labelled cRNA was then fragmented using 5X Array Fragmentation Buffer supplied with the MessageAmp II-Biotin Enhanced Kit.

growth_protocol: Hydroponic systems were used to precisely control Si feeding of plants and to reduce external Si contamination. Seeds of wheat cultivar AC Drummond, chosen for its known high susceptibility to Bgt, were sown in 9-cm pots in a nylon bed consisting of nylon stockings cut into small ribbons. Hydroponic systems were set up to immerse roots for 15 minutes every 30 minutes. The plants were grown in a greenhouse (16 h light at 22°C and 8h dark at 18°C, 80% humidity). Plants were immersed in distilled water only during the first week following sowing.

extract_protocol: Plants were  individually harvested, flash frozen in liquid nitrogen and kept at -80°C until used. Leaves of each plant were separately ground with a pestle and mortar in liquid nitrogen. Total RNA was extracted with RNeasy plant kit (Qiagen, Hilden, Germany). Concentration and quality of RNA were assessed on a Nanodrop spectrophotometer (Nanodrop, Wilmington, De, USA) and 2100 Bioanalyser (Agilent, Palo Alto, Ca, USA).

treatment_protocol: Wheat plants were grown in the presence (Si+) or absence (Si-) of Si and inoculated (B+) or not (B-) with Bgt for a total of four treatments: Si-B-, Si+B-, Si-B+, and Si+B+. These treatments were applied in the following manner. One week after sowing, distilled water was replaced by a Hoagland solution amended or not with potassium silicate (Kasil 6, PQ Corp etc) at a concentration of 1.7 mM (Si+ Hoagland). Twice a week, Si was added to the Si+ nutrient solution in order to maintain Si concentration at 1.7 mM. Every other week, both Si- and Si+ Hoagland solutions were renewed and the pH adjusted to 5.8 in all systems at each Si addition or nutrient solution renewal.   Four weeks after sowing (i.e. three weeks after Si amendment started), half the plants were inoculated with Bgt as described previously. Briefly, one day prior to inoculation, reservoir wheat plants heavily infected with Bgt were gently shaken to remove old spores and to stimulate the production of fresh ones. The inoculation was performed by shaking the heavily infected wheat plants over the experimental plants.

tag: wheat cultivar AC Drummond, age = 7weeks


title: Si+ B+ rep3


title: Si+ B+ rep1


title: I028

value: Asian

value: Ceftriaxone, Fortum,Clindamycin

value: Corynebacterium spp.


title: Si- B- rep3

source_name: no silicon, no disease inoculation


title: Si+ B- rep1

source_name: silicon, no disease inoculation


title: Si- B+ rep2

source_name: no silicon, disease inoculation


title: Si+ B- rep3


title: Si- B+ rep1


title: Si- B- rep1


title: Si+ B- rep2


title: Si- B+ rep3


title: 39

status: Public on Jun 15 2009

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description:
Data from triplicate probes was averaged.  For each probe, see raw data which is supplied as a supplementary file.
We routinely scanned arrays hybridized with Cy5 labeled DNA using both 635 and 532 wavelengths.  The Cy3 channel data in the raw data files for these samples can be deleted as it was not used in any data analysis.

hyb_protocol: Labeled DNA was hybridized to arrays for 14 hrs at 42C.

scan_protocol: The arrays were scanned with a GenePix 4000B

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity of all empty spots on array) was determined.

organism: Clostridium perfringens

source_name: Clostridium perfringens, strain 39

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers using Klenow fragment

extract_protocol: Epicenter MasterPure DNA Purification kit (Madison, WI)

tag: toxin subtype

value: negative


title: Si- B- rep2


title: 251485031874C

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: Agilent Catalog 4by44k whole genome array of TERT cells

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Parent Cell Line (TERT) Reference

extract_protocol: Qiagen Rneasy Mini

treatment_protocol: Pooled harvests of TERT cells grown to 60-80% confluence

value: TERT parent cell line (reference)

growth_protocol: Replicate harvests of TERT cells that stably express siRNA targeted to SFRP1, grown to 60-80% confluence

extract_protocol: Qiagen Rneasy Kit


title: Spo.Young (Rep1-# 19)

status: Public on Jun 16 2009

city: Cambridge

first: Monica

last: Boselli

address: 40 Ames street

department: Center for cancer research

institute: Koch Inst. (KI) MIT

description: vegetatively growing cells

hyb_protocol: According to Dunhan et al.

scan_protocol: Scanned on an Agilent G2565AA scanner according to the Agilent instructions

data_processing: Data points that had FLAG values were discarded. Intentity minimums were floored to the median of 3xSLv1 probe scores. Subtracted data was then median normalized between experiments and duplicate probes were averaged.

organism: Saccharomyces cerevisiae

source_name: Young (age ~ 4 generations) Sporulating cells

label_protocol: Low RNA linear amplification kit from Agilent was used to amplify and label the RNA.

growth_protocol: Control cells were grown in YPD and harvested before they reach OD 1.0. Experimental samples (young and old yeast cells) were grown for 6 hrs in sporulation medium (0.2% KAC) and harvested as described in material and methods.

extract_protocol: Acid phenol RNA extraction was performed according to Dunham M. protocol.Briefly, membranes with the cells were incubated in lysis buffer (10 mM EDTA, 0.5% SDS, and 10 mMTris, pH 7.5) and acid phenol in presence of. The aqueous phase was further extracted twice with an equal volume of chloroform using phase lock gel (Eppendorf). Total RNA was then  ethanol precipitated and further purified over RNeasy columns (Qiagen). RNA quality was checked using the Bioanalyzer RNA Nano kit, and 200 ng was used for microarray labeling with the Agilent Low RNA Input Fluorescent Linear Amplification Kit. Rneasy quigen kit was used for all the RNA purification steps.

treatment_protocol: Cells were harvested, put on a membrane and snap frozen with liquid nitrogen. Agilent arrays 8x15K were used for expression analysis.

tag: age

value: young

tag: medium

value: grown in sporulation medium (0.2% KAC) for 6 hrs

source_name: S. cerevisiae

value: New-born

value: YPD


title: Spo Old (Rep2-#23)

description: vegetatively growing cells

source_name: Old (age ~ 15 generations) Sporulating cells

value: old


title: CDC5262

organism: Clostridium butyricum

source_name: Clostridium butyricum, strain CDC5262


title: Spo.Young (Rep2-#19D)

description: vegetatively growing cells


title: KA9

organism: Clostridium botulinum

source_name: Clostridium botulinum, strain KA9

value: D


title: Spo Old (Rep1-#22)

description: vegetatively growing cells


title: 251485031874D

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

value: TERT cells that stably express siRNA targeted to SFRP1


title: CDC2741

organism: Clostridium argentinense

source_name: Clostridium argentinense, strain CDC2741

value: G


title: 251485031874B


title: 251485031874A


title: CDC35194

source_name: Clostridium botulinum, strain CDC35194

value: F


title: 468

source_name: Clostridium botulinum, strain 468

value: C


title: CDC5247

source_name: Clostridium botulinum, strain CDC5247


title: CDC51192

organism: Clostridium baratii

source_name: Clostridium baratii, strain CDC51192


title: VH-E

source_name: Clostridium botulinum, strain VH-E


title: CDC3281

source_name: Clostridium botulinum, strain CDC3281

value: Bf


title: Beluga

source_name: Clostridium botulinum, strain Beluga


title: Langeland

source_name: Clostridium botulinum, strain Langeland


title: CDC22816

source_name: Clostridium botulinum, strain CDC22816


title: Okra

source_name: Clostridium botulinum, strain Okra


title: CDC59755

source_name: Clostridium botulinum, strain CDC59755

value: A(B)


title: CDC1903

source_name: Clostridium botulinum, strain CDC1903


title: CDC5328

source_name: Clostridium botulinum, strain CDC5328


title: CDC1882

source_name: Clostridium botulinum, strain CDC1882


title: 17B

source_name: Clostridium botulinum, strain 17B

value: Bnp


title: CDC41376

source_name: Clostridium botulinum, strain CDC41376


title: CDC49127

source_name: Clostridium botulinum, strain CDC49127


title: 11439

organism: Clostridium sporogenes

source_name: Clostridium sporogenes, strain 11439


title: BS-A

source_name: Clostridium botulinum, strain BS-A


title: 115B

source_name: Clostridium botulinum, strain 115B


title: CDC297

source_name: Clostridium botulinum, strain CDC297


title: Cam2A

source_name: Clostridium botulinum, strain Cam2A


title: 32A

source_name: Clostridium botulinum, strain 32A


title: DNA Pol2-13MYC rrm3 delete asyn dyeswap 182

city: Princeton

first: Anna

last: Azvolinsky

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

description:
DNA Pol2-MYC
rrm3 delete ChIP-chip from W303a asynchronous cells

hyb_protocol: Microarray hybridizations were performed as previously described (Iyer et al., 2001) at 65ºC for 12 to 16 hours.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with using Genepix 6.1 software.

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were normalized to the median value

source_name: DNA Pol2-13MYC rrm3 delete asyn input DNA

label_protocol: input DNA labelled with Cy5

growth_protocol: W303 DNA Pol2-13MYC tagged rrm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed, and genomic DNA  was purified after reversing crosslinks

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and DNA was isolated

tag: genotype

value: haploid W303a DNA Pol2-13MYC rrm3 delete  cells

source_name: DNA Pol2-13MYC rrm3 delete asyn IP'ed DNA

label_protocol: IP'ed DNA labelled with Cy3

growth_protocol: W303 DNA Pol213MYC tagged rrm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA  Pol2-13MYC using MYC Ab

value: DNA Pol2-MYC expressing rrm3 delete haploid cells


title: DNA Pol2-13MYC rrm3 delete asyn 239

description: DNA Pol2-MYC rrm3 delete ChIP-chip from W303a asynchronous cells

label_protocol: input DNA labelled with Cy3

label_protocol: IP'ed DNA labelled with Cy5

growth_protocol: W303 DNA Pol2-13MYC tagged rrm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA  Pol2-13MYC using MYC Ab.


title: Rrm3-13MYC asyn 041

description: Rrm3-13MYC ChIP-chip from W303a asynchronous cells

source_name: Rrm3-13MYC  asyn input DNA

growth_protocol: W303 Rrm3-13MYC tagged asynchronous cells grown in YEPD rich media to OD of 0.25, fixed, and genomic DNA  was purified after reversing crosslinks

value: haploid W303a Rrm3-13MYC  cells

source_name: Rrm3-13MYC  asyn IP'ed DNA

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP Rrm3-13MYC using MYC Ab.

value: Rrm3-13MYC expressing W303a haploid cells


title: DNA Pol2 asyn 039

description: DNA Pol2-MYC ChIP-chip from W303a asynchronous cells

source_name: input total genomic DNA

label_protocol: Input DNA was labeled using Cy3

growth_protocol: W303 DNA Pol2-13MYC tagged asynchronous cells grown in YEPD rich media to OD of 0.25, fixed, and genomic DNA  was purified after reversing crosslinks

value: haploid W303a cells

source_name: ChIP DNA IP using MYC antibody

label_protocol: IP'ed DNA was labeled using Cy5

value: DNA Pol2-MYC expressing W303a haploid cells


title: Rrm3-13MYC asyn dyeswap 184

description: Rrm3-MYC ChIP-chip from W303a asynchronous cells

growth_protocol: W303 Rrm3-13MYC tagged  asynchronous cells grown in YEPD rich media to OD of 0.25, fixed, and genomic DNA  was purified after reversing crosslinks

growth_protocol: W303 DNA Rrm3-13MYC tagged  asynchronous cells grown in YEPD rich media to OD of 0.25, fixed

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA  Rrm3-13MYC using MYC Ab


title: Rrm3-13MYC asyn dyeswap 185

description: Rrm3-MYC  ChIP-chip from W303a asynchronous cells

growth_protocol: W303 DNA Rrm3-13MYC tagged asynchronous cells grown in YEPD rich media to OD of 0.25, fixed


title: DNA Pol2-13MYC rrm3 delete asyn 040

label_protocol: IP'ed DNa labelled with Cy5

growth_protocol: W303 DNA Pol2-13MYC rrm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed


title: DNA Pol2 asyn 086

source_name: genomic DNA asynchrnous cells

growth_protocol: asynchronous growth in YEPD at 30 degrees

label_protocol: IPed DNA was labeled using Cy5

extract_protocol:
Extract was used for IP with H3K36me2 Ab.
       Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA  Pol2-13MYC using MYC Ab.

treatment_protocol: W303 DNA Pol2-13MYC tagged asynchronous cells grown in YEPD rich media to OD of 0.25, fixed using formaldehyde


title: DNA Pol2 asyn 136

source_name: Input DNA

label_protocol: IP'ed DNA was labelled with Cy5

growth_protocol: W303 DNA Pol2-13MYC tagged asynchronous cells grown in YEPD rich media to OD of 0.25, fixed

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA Pol2-13MYC using MYC Ab.


title: DNA Pol2 asyn 230 dyeswap

source_name: genomic DNA from DNA Pol2-MYC expressing cerevisiae

source_name: DNA Pol2-MYC IP DNA

label_protocol: IP'ed DNA was labelled with Cy3


title: Rrm3-13MYC asyn 088

extract_protocol: Fixed cells were washed and lysed using zymolyase, sonicated to shear chromatin, and extract was used to IP DNA  Rrm3-13MYC using MYC Ab.


title: Keratinocytes, BMP4 treatment

city: Bradford

first: Michael

last: Fessing

state: West Yorkshire

address: Richmond Road

department: Medical Biosciences

country: United Kingdom

institute: University of Bradford

description: Gene expression data  from BMP4 treated keratinocytes

hyb_protocol: 16 hours in GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm)

scan_protocol: Microarray were scand using Affymatrix GeneArray Scanner 3000 7G Plus

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Primary human epidermal keratinocytes, treated with 50 ng/nm BMP4 for 8 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary human epidermal keratinocytes and dermal fibroblasts were isolated from donor forhead skin and cultured under standard conditions.  The cells were passed when they reached 80% confluency

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen),  treated with RNeasy free DNAse I and purified using Rnaesy columns (Qiagen)

treatment_protocol: Cells were used for treatment at the third passage when they reached 50-60 % confluency.  The cells were treated with recombinant BMP4 at final concentration 50 ng/ml or solvent control.

tag: cell type

value: primary cultured epidermal keratinocyte


title: Keratinocytes, control treatment

description: Gene expression data  from control treated keratinocytes

source_name: Primary human epidermal keratinocytes, solvent treated


title: DNA Pol2-13MYC rrm3 delete asyn dyeswap 240


title: Rrm3-13MYC asyn 031


title: DNA Pol2-13MYC rrm3 delete asyn 137

label_protocol: input DNa labelled with Cy3

treatment_protocol: W303 DNA Pol2-13MYC rm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed


title: DNA Pol2-13MYC rrm3 delete asyn dyeswap 183

label_protocol: IP'ed DNa labelled with Cy3

growth_protocol: W303 DNA Pol2-13MYC rm3 delete asynchronous cells grown in YEPD rich media to OD of 0.25, fixed


title: DNA Pol2-13MYC asyn dyeswap 231

source_name: DNA Pol2-13MYC  asyn input DNA

value: haploid W303a DNA Pol2-13MYC  cells

source_name: DNA Pol2-13MYC  asyn IP'ed DNA


title: T253 W3A 24h rep1

status: Public on Jun 14 2009

city: berlin

last: li

address: Robert-Rössle-Straße 10

country: Germany

institute: MAX-DELBRÜCK-CENTRUM FÜR MOLEKULARE MEDIZIN (MDC)

description:
hMSC immortalized by human telomerase.
replicate 1 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalised using cubic spline normalisation with Illumina Beadstudio software.

Non-normalized data are available in the 'GSE16186_non-normalized_data.txt' file, which is linked to the GSE16186 record as a supplementary file.

source_name: mesenchymal stem cell, activated LRP5, Wnt3a medium, 24 hr

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. Quality control was performed with the Agilent Bioanalyzer.

growth_protocol: Cells were cultured in minimum essential medium (MEM, Invitrogen) supplemented with 10% fetal bovine serum (FBS, PAA laboratories), and 1% penicillin/streptomycin.

extract_protocol: RNA was isolated by the RNeasy mini kit (Qiagen), followed by DNase I treatment with the same kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: Cells were treated with 50% control condition medium or Wnt3a condition medium for 1 hour or 24 hours.

value: mesenchymal stem cell

tag: form of overexpressed lrp5

value: activated

tag: treatment

value: Wnt3a conditioned medium

tag: treatment time

value: 24 hr


title: T253 W3A 24h rep3

description:
hMSC immortalized by human telomerase.
replicate 3 of 3.


title: Fibroblasts, control treatment

description: Gene expression data  from control treated fibroblasts

source_name: Primary human dermal fibroblasts, solvent treated

value: primary cultured dermal fibroblast


title: T253 W3A 24h rep2

description:
hMSC immortalized by human telomerase.
replicate 2 of 3.


title: T253 Co 24h rep3

source_name: mesenchymal stem cell, activated LRP5, control medium, 24 hr

value: control conditioned medium


title: Fibroblasts, BMP4 treatment

description: Gene expression data  from BMP4 treated fibroblasts

source_name: Primary human dermal fibroblasts, treated with 50 ng/nm BMP4 for 8 hours


title: T244 W3A 24h rep3

source_name: mesenchymal stem cell, inactivated LRP5, Wnt3a medium, 24 hr

value: inactivated


title: T244 Co 24h rep2

source_name: mesenchymal stem cell, inactivated LRP5, control medium, 24 hr


title: T253 W3A 1h rep3

source_name: mesenchymal stem cell, activated LRP5, Wnt3a medium, 1 hr

value: 1 hr


title: T244 Co 24h rep1


title: T253 Co 1h rep3

source_name: mesenchymal stem cell, activated LRP5, control medium, 1 hr


title: T244 Co 24h rep3


title: T244 W3A 1h rep3

source_name: mesenchymal stem cell, inactivated LRP5, Wnt3a medium, 1 hr


title: T253 Co 1h rep1


title: T244 W3A 24h rep2


title: T253 Co 24h rep2


title: T244 W3A 24h rep1


title: T253 W3A 1h rep2


title: T253 Co 1h rep2


title: T253 Co 24h rep1


title: T253 W3A 1h rep1


title: T244 W3A 1h rep2


title: T244 Co 1h rep2

source_name: mesenchymal stem cell, inactivated LRP5, control medium, 1 hr


title: T244 Co 1h rep3


title: T244 Co 1h rep1


title: T244 W3A 1h rep1


title: mutated IGVH3-23 repl 4

status: Public on Jun 13 2009

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description: Biological replicate 4 of 5.

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile

source_name: Mutated purified cell of CLL

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy5-labeled reference aRNA (according to Agilent protocol)

extract_protocol: Total RNA was extracted according to TRIZOL reagent protocol

value: Mutated purified cell of CLL

source_name: aRNA from pooled normal PB B cells of healthy donors

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)

tag: reference


title: mutated IGVH3-23 repl 3

description: Biological replicate 3 of 5.

value: aRNA from pooled normal PB B cells of healthy donors


title: mutated IGVH3-23 repl 5

description: Biological replicate 5 of 5.


title: mutated IGVH3-23 repl 2

description: Biological replicate 2 of 5.


title: Epidermis_Ras_30 Days 4OHT_IgG-treated_rep2

status: Public on Jun 02 2009

city: Stanford

first: Paul

middle: A

last: Khavari

state: CA

address: 259 Campus Dr

department: Dermatology

institute: Stanford University

description:
Regenerated human epidermis
IgG_control_B

hyb_protocol: Samples were hybridized by the Stanford P.A.N. facility using a Fluidics Station 450 and GeneChip Hybridization Oven 640 following manufacturer's instruction (GeneChip Expression Analysis Technical Manual Rev.2, Affymetrix). For the fluidics protocol, a Midi_euk2v3_450 script was used.

scan_protocol: Samples were scanned by the Stanford P.A.N. facility a on Affymetrix Scanner 3000 G7 (default target signal set at 500).  Also, for the fluidics protocol, we used Midi_euk2v3_450.

data_processing: The raw cel files were imported into GeneSpring 7 (Agilent) and RMA normalized. The only other normalization that was applied was setting values less than 0.01 to 0.01.

source_name: epidermis, 30 days Ras activation, +4OHT, IgG injected

label_protocol: Total RNA was amplified and fragmented using Message Amp II-Biotin following manufacturer's instruction (Ambion). 100-200ng of total RNA was amplified using 16 hr IVT reaction.

growth_protocol: Epidermal tissue co-expressing ER:H-RasG12V and IkBaM was regenerated on female scid/scid mouse recipients. Grafts were allowed to heal for at least 3 weeks before Ras activation via daily i.p. injections of 730ug of 4OHT (in 110ul of a corn oil/ethanol mixture).  Duplicate grafts were harvested after  0, 5, 20, and 35 days of 4OHT treatment.

extract_protocol: Total RNA was extracted from laser capture microdissected tissue using RNAqueous kit following manufacturer's instruction (Ambion)

treatment_protocol: Tissue was excised and frozen immediately in OCT on dry ice and stored at -20C from weeks to months. Prior to LCM, tissue was sectioned (6um) and stored at -20C for up to 4 days. Sections were stained with cresyl-violet (LCM staining kit, Ambion) and immediately processed by laser capture microdissection. Slides were not allowed to sit more than 2.5 hours at room temp for processing.

tag: tissue

value: Regenerated human epidermis

tag: recipient strain

value: CB-17 scid/scid


title: mutated IGVH3-23 repl 1

description: Biological replicate 1 of 5.


title: Epidermis_Raf_30 Days 4OHT_rep2

description:
Regenerated human epidermis
Raf(+4OHT)_B

source_name: epidermis, 30 days Raf activation, +4OHT


title: Epidermis_Ras_30 Days 4OHT_IgG-treated_rep1

description:
Regenerated human epidermis
IgG_control_A


title: Epidermis_Ras_30 Days 4OHT_anti-b1-treated_rep2

description:
Regenerated human epidermis
b1_blockade_B

source_name: epidermis, 30 days Ras activation, +4OHT, anti-b1 injected


title: Epidermis_Raf_0 Days 4OHT_rep1

description:
Regenerated human epidermis
Raf(-4OHT)_A

source_name: epidermis, 0 days Raf activation, -4OHT


title: Epidermis_Raf_0 Days 4OHT_rep2

description:
Regenerated human epidermis
Raf(-4OHT)_B


title: Epidermis_Ras_30 Days 4OHT_anti-b1-treated_rep1

description:
Regenerated human epidermis
b1_blockade_A


title: Epidermis_Raf_30 Days 4OHT_rep1

description:
Regenerated human epidermis
Raf(+4OHT)_A


title: Epidermis_Ras_20 Days 4OHT_rep1

description:
Regenerated human epidermis
Ras_20Days_A

source_name: epidermis, 20 days Ras activation, +4OHT


title: Epidermis_Ras_35 Days 4OHT_rep2

description:
Regenerated human epidermis
Ras_35Days_B

source_name: epidermis, 35 days Ras activation, +4OHT


title: Epidermis_Ras_20 Days 4OHT_rep2

description:
Regenerated human epidermis
Ras_20Days_B


title: Epidermis_Ras_35 Days 4OHT_rep1

description:
Regenerated human epidermis
Ras_35Days_A


title: Stroma_Ras_35 Days 4OHT_rep2

description:
Adjacent Mouse Stroma
Stroma_35Days_B

organism: Mus musculus

source_name: stroma, 35 days Ras activation, +4OHT

value: Mouse Stroma


title: Epidermis_Ras_0 Days 4OHT_rep1

description:
Regenerated human epidermis
Ras_0Days_A

source_name: epidermis, 0 days Ras activation, -4OHT


title: Epidermis_Ras_0 Days 4OHT_rep2

description:
Regenerated human epidermis
Ras_0Days_B


title: Epidermis_Ras_5 Days 4OHT_rep2

description:
Regenerated human epidermis
Ras_5Days_B

source_name: epidermis, 5 days Ras activation, +4OHT


title: Epidermis_Ras_5 Days 4OHT_rep1

description:
Regenerated human epidermis
Ras_5Days_A


title: Stroma_Ras_20 Days 4OHT_rep1

description:
Adjacent Mouse Stroma
Stroma_20Days_A

source_name: stroma, 20 days Ras activation, +4OHT


title: Stroma_Ras_35 Days 4OHT_rep1

description:
Adjacent Mouse Stroma
Stroma_35Days_A


title: Stroma_Ras_5 Days 4OHT_rep2

description:
Adjacent Mouse Stroma
Stroma_5Days_B

source_name: stroma, 5 days Ras activation, +4OHT


title: Stroma_Ras_20 Days 4OHT_rep2

description:
Adjacent Mouse Stroma
Stroma_20Days_B


title: Stroma_Ras_5 Days 4OHT_rep1

description:
Adjacent Mouse Stroma
Stroma_5Days_A


title: AV node myocardium _ stage e17.5 _ biorep6

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: standard Illumina hybridization protocol

data_processing: Data were processed using the R/Limma package (Bioconductor). Data were normalized using VSN transformation.

source_name: AV node myocardium, stage e17.5, biorep6

growth_protocol: normal development

extract_protocol: For every sample, transgenic hearts were dissected, the GFP-positive tissues pooled, dissociated to obtain single cells, and purified using FACS. 5000 cells per sample were gated and used for RNA isolation (Macherey-Nagel, nucleospin II). RNA was subjected to 2 rounds of linear amplification and biotin labeling (Ambion). Within each group 6 labeled antisense RNA samples were hybridized to separate Illumina Mouse-Ref-6 v1.1 BeadChips.

tag: AV node myocardium

tag: stage


title: Stroma_Ras_0 Days 4OHT_rep1

description:
Adjacent Mouse Stroma
Stroma_0Days_A

source_name: stroma, 0 days Ras activation, -4OHT


title: working myocardium _ stage e17.5 _ biorep5

scan_protocol: standard Illumina hybridization protocol

source_name: working myocardium, stage e17.5, biorep5

label_protocol: RNA was subjected to 2 rounds of linear amplification and biotin labeling (Ambion). Within each group 6 labeled antisense RNA samples were hybridized to separate Illumina Mouse-Ref-6 v1.1 BeadChips.

tag: working myocardium


title: AV node myocardium _ stage e17.5 _ biorep4

source_name: AV node myocardium, stage e17.5, biorep4


title: AV node myocardium _ stage e17.5 _ biorep3

source_name: AV node myocardium, stage e17.5, biorep3


title: working myocardium _ stage e17.5 _ biorep4

source_name: working myocardium, stage e17.5, biorep4


title: AV node myocardium _ stage e17.5 _ biorep2

source_name: AV node myocardium, stage e17.5, biorep2


title: AV node myocardium _ stage e17.5 _ biorep5

source_name: AV node myocardium, stage e17.5, biorep5


title: working myocardium _ stage e17.5 _ biorep3

source_name: working myocardium, stage e17.5, biorep3


title: LB-1

status: Public on Jun 10 2009

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: The growth experiments and RNA extractions were preformed at the Technical University of Denmark. The cDNA synthesis, labelling, hybridization and scanning was performed at NimbleGen.

hyb_protocol: Hybridization was performed using a MAUI Hybridization System at 42C overnight.

scan_protocol: GenePix 4000B Scanner at 532 nm

data_processing: Normalized values were generated by normalizing the raw data with "Qspline" using R and Bioconductor (affy package). No background correction were used.

source_name: Bacillus subtilis, mid-exponential growth in LB

label_protocol: For the reverse transcription reactions Invitrogen Superscript Double-Stranded cDNA Synthesis Kit was used and in the presence of 40 ug/mL Actinomycin D to prevent antisense artifacts. First strand cDNA were synthesised using random primers and each cDNA strand were labelled using Cy3 using Klenow Enzyme and Cy3-labelled 9-mer primers.

growth_protocol: Bacillus subtilis subsp. subtilis str. 168 grown in Luria-Broth medium at 37C, 120rpm. Cells harvested at OD600 = 0.5

extract_protocol: A total of 25 mL from each culture was transferred to a 40 mL tube 1/3-filled with crushed ice and spun at 7,000 rpm for 5 minutes, after which the supernatant was discarded and the cell pellet frozen by dumping the closed tube into liquid nitrogen. Total RNA was extracted by the use of the FastRNA PRO Blue Kit from Qbiogene as recommended by the supplier, but with an additional shake in the FastPrep instrument and a one minute incubation on ice between the two shakings.

tag: growth medium

value: Luria-Broth medium


title: working myocardium _ stage e17.5 _ biorep1

source_name: working myocardium, stage e17.5, biorep1


title: working myocardium _ stage e10.5 _ biorep6

source_name: working myocardium, stage e10.5, biorep6


title: M9-2

source_name: Bacillus subtilis, mid-exponential growth in M9

growth_protocol: Bacillus subtilis subsp. subtilis str. 168 grown in M9 minimal medium at 37C, 120rpm. Cells harvested at OD600 = 0.5

value: M9 minimal medium


title: AV canal myocardium _ stage e10.5 _ biorep5

source_name: AV canal myocardium, stage e10.5, biorep5

tag: AV canal myocardium


title: AV canal myocardium _ stage e10.5 _ biorep6

source_name: AV canal myocardium, stage e10.5, biorep6


title: working myocardium _ stage e10.5 _ biorep3

source_name: working myocardium, stage e10.5, biorep3


title: working myocardium _ stage e10.5 _ biorep5

source_name: working myocardium, stage e10.5, biorep5


title: AV canal myocardium _ stage e10.5 _ biorep2

source_name: AV canal myocardium, stage e10.5, biorep2


title: LB-2

organism: Bacillus subtilis subsp. subtilis str. 168


title: Stroma_Ras_0 Days 4OHT_rep2

description:
Adjacent Mouse Stroma
Stroma_0Days_B

source_name: stroma, 0 days Ras activation, -4OHT


title: working myocardium _ stage e17.5 _ biorep6

source_name: working myocardium, stage e17.5, biorep6


title: LB-3


title: AV canal myocardium _ stage e10.5 _ biorep3

source_name: AV canal myocardium, stage e10.5, biorep3


title: gDNA-3

description: The growth experiments and DNA extractions were preformed at the Technical University of Denmark. The cDNA synthesis, labelling, hybridization and scanning was performed at NimbleGen.

hyb_protocol: Hybridization was performed using a MAUI Hybridization System at 42C overnight using NimbleGen standard protocols. Washing was performed using NimbleGen Wash Buffer Kit according to manufacturers instructions.

label_protocol: Genomic DNA was fragmented using a Branson model 450 Sonifier to size range of ~500bp to 2,000bp. This was labelled using Klenow Enzyme and Cy3-labelled 9mer primers using NimbleGen standard protocols.

extract_protocol: DNA was extracted using the DNeasy Blood tissue kit from Qiagen as recommended by the supplier from 2 mL culture at OD600 = 0.5.


title: M9-3


title: AV canal myocardium _ stage e10.5 _ biorep4

source_name: AV canal myocardium, stage e10.5, biorep4


title: working myocardium _ stage e17.5 _ biorep2

source_name: working myocardium, stage e17.5, biorep2


title: working myocardium _ stage e10.5 _ biorep2

source_name: working myocardium, stage e10.5, biorep2


title: AV canal myocardium_ stage e10.5 _ biorep1

source_name: AV canal myocardium, stage e10.5, biorep1


title: working myocardium _ stage e10.5 _ biorep1

source_name: working myocardium, stage e10.5, biorep1


title: working myocardium _ stage e10.5 _ biorep4

source_name: working myocardium, stage e10.5, biorep4


title: AV node myocardium _ stage e17.5 _ biorep1

source_name: AV node myocardium, stage e17.5, biorep1